Ditto HyLyte's rec of Transatlantic Diesel -- Sheri Moon is good people, and they are a great source for parts and info.
A few other sources:
Parts4Engines: Perkins Diesel Engine Overhaul Kits and Spares
is an on-line retailer in the UK. They stock a smaller supply of parts, but sometimes they are way less expensive (like for the Bowman heat exchanger rubber end caps.)
Stewart's Marine, Inc in Seattle.
Check locally for agricultural/industrial diesel dealers. The 4.108 was used in many skid steers (Massey-Ferguson, Bobcat, etc.) a few tractors, and also to drive agricultural irrigation pumps. Many of the basic engine parts are the same.
As far as your water pump goes, rebuild kits are no longer available. You need to order a new pump (part number U5MW0054.) Think ahead on this one. Getting the pulley off of the old pump without breaking it is the key. Getting the new pulley back on is best done with a shop press so you can get it perfectly aligned with the crank pulley. You may want to consider biting the bullet and buying another pulley and have it pressed on and ready to install should you need to swap out the pump away from a garage.